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RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library.
Guo Y, Zhao S, Sheng Q, Guo M, Lehmann B, Pietenpol J, Samuels DC, Shyr Y
(2015) Biomed Res Int 2015: 862130
MeSH Terms: Gene Expression Profiling, Gene Library, Humans, Open Reading Frames, Poly A, RNA, RNA, Ribosomal, Sequence Analysis, RNA
Show Abstract · Added February 15, 2016
The most popular RNA library used for RNA sequencing is the poly(A) captured RNA library. This library captures RNA based on the presence of poly(A) tails at the 3' end. Another type of RNA library for RNA sequencing is the total RNA library which differs from the poly(A) library by capture method and price. The total RNA library costs more and its capture of RNA is not dependent on the presence of poly(A) tails. In practice, only ribosomal RNAs and small RNAs are washed out in the total RNA library preparation. To evaluate the ability of detecting RNA for both RNA libraries we designed a study using RNA sequencing data of the same two breast cancer cell lines from both RNA libraries. We found that the RNA expression values captured by both RNA libraries were highly correlated. However, the number of RNAs captured was significantly higher for the total RNA library. Furthermore, we identify several subsets of protein coding RNAs that were not captured efficiently by the poly(A) library. One of the most noticeable is the histone-encode genes, which lack the poly(A) tail.
1 Communities
3 Members
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8 MeSH Terms
Oxidative cyclizations in orthosomycin biosynthesis expand the known chemistry of an oxygenase superfamily.
McCulloch KM, McCranie EK, Smith JA, Sarwar M, Mathieu JL, Gitschlag BL, Du Y, Bachmann BO, Iverson TM
(2015) Proc Natl Acad Sci U S A 112: 11547-52
MeSH Terms: Aminoglycosides, Anti-Bacterial Agents, Catalytic Domain, Crystallography, X-Ray, Cyclization, Hydrogen, Hygromycin B, Metals, Micromonospora, Multigene Family, Oligosaccharides, Open Reading Frames, Oxidation-Reduction, Oxygen, Oxygenases, Phylogeny, Protein Binding, Protein Structure, Secondary, Reproducibility of Results, Streptomyces
Show Abstract · Added April 1, 2019
Orthosomycins are oligosaccharide antibiotics that include avilamycin, everninomicin, and hygromycin B and are hallmarked by a rigidifying interglycosidic spirocyclic ortho-δ-lactone (orthoester) linkage between at least one pair of carbohydrates. A subset of orthosomycins additionally contain a carbohydrate capped by a methylenedioxy bridge. The orthoester linkage is necessary for antibiotic activity but rarely observed in natural products. Orthoester linkage and methylenedioxy bridge biosynthesis require similar oxidative cyclizations adjacent to a sugar ring. We have identified a conserved group of nonheme iron, α-ketoglutarate-dependent oxygenases likely responsible for this chemistry. High-resolution crystal structures of the EvdO1 and EvdO2 oxygenases of everninomicin biosynthesis, the AviO1 oxygenase of avilamycin biosynthesis, and HygX of hygromycin B biosynthesis show how these enzymes accommodate large substrates, a challenge that requires a variation in metal coordination in HygX. Excitingly, the ternary complex of HygX with cosubstrate α-ketoglutarate and putative product hygromycin B identified an orientation of one glycosidic linkage of hygromycin B consistent with metal-catalyzed hydrogen atom abstraction from substrate. These structural results are complemented by gene disruption of the oxygenases evdO1 and evdMO1 from the everninomicin biosynthetic cluster, which demonstrate that functional oxygenase activity is critical for antibiotic production. Our data therefore support a role for these enzymes in the production of key features of the orthosomycin antibiotics.
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MeSH Terms
Revealing Missing Human Protein Isoforms Based on Ab Initio Prediction, RNA-seq and Proteomics.
Hu Z, Scott HS, Qin G, Zheng G, Chu X, Xie L, Adelson DL, Oftedal BE, Venugopal P, Babic M, Hahn CN, Zhang B, Wang X, Li N, Wei C
(2015) Sci Rep 5: 10940
MeSH Terms: Algorithms, Alternative Splicing, Computational Biology, Datasets as Topic, Humans, Open Reading Frames, Protein Isoforms, Proteomics, Reproducibility of Results, Sequence Analysis, RNA, Transcription, Genetic
Show Abstract · Added February 15, 2016
Biological and biomedical research relies on comprehensive understanding of protein-coding transcripts. However, the total number of human proteins is still unknown due to the prevalence of alternative splicing. In this paper, we detected 31,566 novel transcripts with coding potential by filtering our ab initio predictions with 50 RNA-seq datasets from diverse tissues/cell lines. PCR followed by MiSeq sequencing showed that at least 84.1% of these predicted novel splice sites could be validated. In contrast to known transcripts, the expression of these novel transcripts were highly tissue-specific. Based on these novel transcripts, at least 36 novel proteins were detected from shotgun proteomics data of 41 breast samples. We also showed L1 retrotransposons have a more significant impact on the origin of new transcripts/genes than previously thought. Furthermore, we found that alternative splicing is extraordinarily widespread for genes involved in specific biological functions like protein binding, nucleoside binding, neuron projection, membrane organization and cell adhesion. In the end, the total number of human transcripts with protein-coding potential was estimated to be at least 204,950.
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11 MeSH Terms
Evaluating the Merits of CKD Patient Educational Materials: Readability Is Necessary But Not Sufficient.
Tuot DS, Cavanaugh KL
(2015) Am J Kidney Dis 65: 814-6
MeSH Terms: Comprehension, Humans, Internet, Patient Education as Topic, Reading, Renal Insufficiency, Chronic, Teaching Materials
Added August 4, 2015
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7 MeSH Terms
Teaching reading to children with neurofibromatosis type 1: a clinical trial with random assignment to different approaches.
Barquero LA, Sefcik AM, Cutting LE, Rimrodt SL
(2015) Dev Med Child Neurol 57: 1150-8
MeSH Terms: Adolescent, Child, Dyslexia, Education, Special, Female, Humans, Male, Neurofibromatosis 1, Reading, Treatment Outcome
Show Abstract · Added February 15, 2016
AIM - Neurofibromatosis type 1 (NF1) is a genetic disorder with a cognitive profile that includes visual-spatial perception deficits and a high incidence of reading disability. There is a paucity of information about how this cognitively complex population responds to mainstream reading interventions. The clinical trial goals were to determine whether children and adolescents with NF1 and reading deficits (NF+RD) benefit from mainstream remedial reading programs and whether responsiveness varies with differences in program-related visual-spatial demands.
METHOD - Forty-nine participants (28 males, 21 females; aged 8-14y) with either NF+RD (n=17, 11 males, six females) or idiopathic reading deficit (IRD) (n=32, 17 males, 15 females) were randomly assigned to intensive remedial teaching using one of two multisensory reading programs: one with greater kinesthetic demands and the other with greater visual-spatial demands. Two control groups - wait-list IRD (n=14, 11 males, three females) and typically developing readers (n=26, 13 males, 13 females) - received no treatment. Repeated measures and multivariate ANOVA analyses compared each group's growth in reading achievement from pre- to post-testing.
RESULTS - Treated groups showed significant growth whereas untreated groups did not. Comparing treated groups, the IRD group responded equally well to both interventions, whereas the NF+RD group showed a better response to the more kinesthetic approach.
INTERPRETATION - Results suggest that multisensory remedial reading teaching that emphasizes kinesthetic demands more than visual-spatial demands is suitable for students with NF+RD.
© 2015 Mac Keith Press.
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10 MeSH Terms
Longitudinal stability in reading comprehension is largely heritable from grades 1 to 6.
Soden B, Christopher ME, Hulslander J, Olson RK, Cutting L, Keenan JM, Thompson LA, Wadsworth SJ, Willcutt EG, Petrill SA
(2015) PLoS One 10: e0113807
MeSH Terms: Child, Comprehension, Female, Genetic Association Studies, Humans, Longitudinal Studies, Male, Models, Theoretical, Ohio, Reading, Schools, Twins
Show Abstract · Added February 15, 2016
Reading comprehension is a foundational academic skill and significant attention has focused on reading development. This report is the first to examine the stability and change in genetic and environmental influences on reading comprehension across Grades 1 to 6. This developmental range is particularly important because it encompasses the timespan in which most children move from learning how to read to using reading for learning. Longitudinal simplex models were fitted separately for two independent twin samples (N = 706; N = 976). Results suggested that the shared environment contributed to variance in early but not later reading. Instead, stability in reading development was largely mediated by continuous genetic influences. Thus, although reading is clearly a learned skill and the environment remains important for reading development, individual differences in reading comprehension appear to be also influenced by a core of genetic stability that persists through the developmental course of reading.
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12 MeSH Terms
Upstream open reading frame in 5'-untranslated region reduces titin mRNA translational efficiency.
Cadar AG, Zhong L, Lin A, Valenzuela MO, Lim CC
(2014) Biochem Biophys Res Commun 453: 185-91
MeSH Terms: 5' Untranslated Regions, Animals, Base Sequence, Cell Line, Connectin, Doxorubicin, Gene Expression Regulation, HEK293 Cells, Half-Life, Humans, Mice, Molecular Sequence Data, Myocytes, Cardiac, Open Reading Frames, Polymorphism, Single Nucleotide, Protein Kinases, RNA Stability, RNA, Messenger, Rats, Sarcomeres, Sequence Homology, Nucleic Acid
Show Abstract · Added February 19, 2015
Titin is the largest known protein and a critical determinant of myofibril elasticity and sarcomere structure in striated muscle. Accumulating evidence that mRNA transcripts are post-transcriptionally regulated by specific motifs located in the flanking untranslated regions (UTRs) led us to consider the role of titin 5'-UTR in regulating its translational efficiency. Titin 5'-UTR is highly homologous between human, mouse, and rat, and sequence analysis revealed the presence of a stem-loop and two upstream AUG codons (uAUGs) converging on a shared in frame stop codon. We generated a mouse titin 5'-UTR luciferase reporter construct and targeted the stem-loop and each uAUG for mutation. The wild-type and mutated constructs were transfected into the cardiac HL-1 cell line and primary neonatal rat ventricular myocytes (NRVM). SV40 driven 5'-UTR luciferase activity was significantly suppressed by wild-type titin 5'-UTR (∼ 70% in HL-1 cells and ∼ 60% in NRVM). Mutating both uAUGs was found to alleviate titin 5'-UTR suppression, while eliminating the stem-loop had no effect. Treatment with various growth stimuli: pacing, PMA or neuregulin had no effect on titin 5'-UTR luciferase activity. Doxorubicin stress stimuli reduced titin 5'-UTR suppression, while H2O2 had no effect. A reported single nucleotide polymorphism (SNP) rs13422986 at position -4 of the uAUG2 was introduced and found to further repress titin 5'-UTR luciferase activity. We conclude that the uAUG motifs in titin 5'-UTR serve as translational repressors in the control of titin gene expression, and that mutations/SNPs of the uAUGs or doxorubicin stress could alter titin translational efficiency.
Copyright © 2014 Elsevier Inc. All rights reserved.
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21 MeSH Terms
Structural connectivity patterns associated with the putative visual word form area and children's reading ability.
Fan Q, Anderson AW, Davis N, Cutting LE
(2014) Brain Res 1586: 118-29
MeSH Terms: Agnosia, Brain Mapping, Cerebral Cortex, Child, Female, Functional Laterality, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, Oxygen, Reading, Visual Perception, Vocabulary
Show Abstract · Added January 20, 2015
With the advent of neuroimaging techniques, especially functional MRI (fMRI), studies have mapped brain regions that are associated with good and poor reading, most centrally a region within the left occipito-temporal/fusiform region (L-OT/F) often referred to as the visual word form area (VWFA). Despite an abundance of fMRI studies of the putative VWFA, research about its structural connectivity has just started. Provided that the putative VWFA may be connected to distributed regions in the brain, it remains unclear how this network is engaged in constituting a well-tuned reading circuitry in the brain. Here we used diffusion MRI to study the structural connectivity patterns of the putative VWFA and surrounding areas within the L-OT/F in children with typically developing (TD) reading ability and with word recognition deficits (WRD; sometimes referred to as dyslexia). We found that L-OT/F connectivity varied along a posterior-anterior gradient, with specific structural connectivity patterns related to reading ability in the ROIs centered upon the putative VWFA. Findings suggest that the architecture of the putative VWFA connectivity is fundamentally different between TD and WRD, with TD showing greater connectivity to linguistic regions than WRD, and WRD showing greater connectivity to visual and parahippocampal regions than TD. Findings thus reveal clear structural abnormalities underlying the functional abnormalities in the putative VWFA in WRD.
Copyright © 2014 Elsevier B.V. All rights reserved.
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14 MeSH Terms
A perceptual learning deficit in Chinese developmental dyslexia as revealed by visual texture discrimination training.
Wang Z, Cheng-Lai A, Song Y, Cutting L, Jiang Y, Lin O, Meng X, Zhou X
(2014) Dyslexia 20: 280-96
MeSH Terms: Attention, Child, China, Discrimination Learning, Dyslexia, Female, Humans, Learning Disabilities, Male, Orientation, Pattern Recognition, Visual, Reading, Semantics, Visual Perception
Show Abstract · Added May 27, 2014
Learning to read involves discriminating between different written forms and establishing connections with phonology and semantics. This process may be partially built upon visual perceptual learning, during which the ability to process the attributes of visual stimuli progressively improves with practice. The present study investigated to what extent Chinese children with developmental dyslexia have deficits in perceptual learning by using a texture discrimination task, in which participants were asked to discriminate the orientation of target bars. Experiment l demonstrated that, when all of the participants started with the same initial stimulus-to-mask onset asynchrony (SOA) at 300 ms, the threshold SOA, adjusted according to response accuracy for reaching 80% accuracy, did not show a decrement over 5 days of training for children with dyslexia, whereas this threshold SOA steadily decreased over the training for the control group. Experiment 2 used an adaptive procedure to determine the threshold SOA for each participant during training. Results showed that both the group of dyslexia and the control group attained perceptual learning over the sessions in 5 days, although the threshold SOAs were significantly higher for the group of dyslexia than for the control group; moreover, over individual participants, the threshold SOA negatively correlated with their performance in Chinese character recognition. These findings suggest that deficits in visual perceptual processing and learning might, in part, underpin difficulty in reading Chinese.
Copyright © 2014 John Wiley & Sons, Ltd.
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14 MeSH Terms
An expressed retrogene of the master embryonic stem cell gene POU5F1 is associated with prostate cancer susceptibility.
Breyer JP, Dorset DC, Clark TA, Bradley KM, Wahlfors TA, McReynolds KM, Maynard WH, Chang SS, Cookson MS, Smith JA, Schleutker J, Dupont WD, Smith JR
(2014) Am J Hum Genet 94: 395-404
MeSH Terms: Adolescent, Adult, Aged, Alleles, Case-Control Studies, Cell Nucleus, Cell Transformation, Neoplastic, Databases, Genetic, Embryonic Stem Cells, Gene Expression Regulation, Neoplastic, Genetic Predisposition to Disease, Genetic Variation, Genotype, Haplotypes, Humans, Male, Middle Aged, Mutation, Missense, Octamer Transcription Factor-3, Open Reading Frames, Prostatic Neoplasms, Quantitative Trait Loci, Risk, Sequence Analysis, DNA, Transcription, Genetic, Young Adult
Show Abstract · Added March 20, 2014
Genetic association studies of prostate and other cancers have identified a major risk locus at chromosome 8q24. Several independent risk variants at this locus alter transcriptional regulatory elements, but an affected gene and mechanism for cancer predisposition have remained elusive. The retrogene POU5F1B within the locus has a preserved open reading frame encoding a homolog of the master embryonic stem cell transcription factor Oct4. We find that 8q24 risk alleles are expression quantitative trait loci correlated with reduced expression of POU5F1B in prostate tissue and that predicted deleterious POU5F1B missense variants are also associated with risk of transformation. POU5F1 is known to be self-regulated by the encoded Oct4 transcription factor. We further observe that POU5F1 expression is directly correlated with POU5F1B expression. Our results suggest that a pathway critical to self-renewal of embryonic stem cells may also have a role in the origin of cancer.
Copyright © 2014 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.
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26 MeSH Terms